From 6de576b4e8292ab0610fb810b505e7a082596b01 Mon Sep 17 00:00:00 2001
From: Tomas Lovato <tomas.lovato@cmcc.it>
Date: Fri, 25 Feb 2022 11:21:01 +0100
Subject: [PATCH] revise most of the items in Additions, deletions and
corrections
---
doc/latex/NEMO/subfiles/chap_DIA.tex | 9 +++---
doc/latex/NEMO/subfiles/chap_DYN.tex | 26 -----------------
doc/latex/NEMO/subfiles/chap_SBC.tex | 40 ++-------------------------
doc/latex/NEMO/subfiles/chap_cfgs.tex | 2 +-
doc/latex/NEMO/subfiles/chap_misc.tex | 4 +--
5 files changed, 11 insertions(+), 70 deletions(-)
diff --git a/doc/latex/NEMO/subfiles/chap_DIA.tex b/doc/latex/NEMO/subfiles/chap_DIA.tex
index c8f36b62..b6508dbe 100644
--- a/doc/latex/NEMO/subfiles/chap_DIA.tex
+++ b/doc/latex/NEMO/subfiles/chap_DIA.tex
@@ -1464,7 +1464,7 @@ In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor
and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}).
%% =================================================================================================
-\section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]{FLO: On-Line Floats trajectories (\protect\key{floats})}
+\section[FLO: On-Line Floats trajectories]{FLO: On-Line Floats trajectories}
\label{sec:DIA_FLO}
\begin{listing}
@@ -1475,7 +1475,8 @@ and none of the options have been tested with variable volume (\ie\ \np[=.true.]
The on-line computation of floats advected either by the three dimensional velocity field or constraint to
remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project.
-Options are defined by \nam{flo}{flo} namelist variables.
+Options are defined by \nam{flo}{flo} namelist variables and the interface is activated by setting \np{ln_float = .true.}.
+
The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option),
or on a $4^th$ Runge-Hutta algorithm (\np[=.true.]{ln_flork4}{ln\_flork4}).
Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which
@@ -1567,7 +1568,7 @@ Here it is an example of specification to put in files description section:
\end{xmllines}
%% =================================================================================================
-\section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})}
+\section[Transports across sections]{Transports across sections}
\label{sec:DIA_diag_dct}
\begin{listing}
@@ -1577,7 +1578,7 @@ Here it is an example of specification to put in files description section:
\end{listing}
A module is available to compute the transport of volume, heat and salt through sections.
-This diagnostic is actived with \key{diadct}.
+This diagnostic is actived with \np{ln_diadct = .true.}.
Each section is defined by the coordinates of its 2 extremities.
The pathways between them are contructed using tools which can be found in \texttt{tools/SECTIONS\_DIADCT}
diff --git a/doc/latex/NEMO/subfiles/chap_DYN.tex b/doc/latex/NEMO/subfiles/chap_DYN.tex
index 4d82795d..f61cdb29 100644
--- a/doc/latex/NEMO/subfiles/chap_DYN.tex
+++ b/doc/latex/NEMO/subfiles/chap_DYN.tex
@@ -1057,32 +1057,6 @@ the filter \autoref{eq:DYN_spg_ts_sshf} was found to be more conservative, and s
} %%end gm comment (copy of griffies book)
-%% =================================================================================================
-\subsection{Filtered free surface (\forcode{dynspg_flt?})}
-\label{subsec:DYN_spg_fltp}
-
-The filtered formulation follows the \citet{roullet.madec_JGR00} implementation.
-The extra term introduced in the equations (see \autoref{subsec:MB_free_surface}) is solved implicitly.
-The elliptic solvers available in the code are documented in \autoref{chap:MISC}.
-
-%% gm %%======>>>> given here the discrete eqs provided to the solver
-\cmtgm{ %%% copy from chap-model basics
- \[
- % \label{eq:DYN_spg_flt}
- \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= {\mathrm {\mathbf M}}
- - g \nabla \left( \tilde{\rho} \ \eta \right)
- - g \ T_c \nabla \left( \widetilde{\rho} \ \partial_t \eta \right)
- \]
- where $T_c$, is a parameter with dimensions of time which characterizes the force,
- $\widetilde{\rho} = \rho / \rho_o$ is the dimensionless density,
- and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient,
- non-linear and viscous terms in \autoref{eq:MB_dyn}.
-} %end cmtgm
-
-Note that in the linear free surface formulation (\texttt{vvl?} not defined),
-the ocean depth is time-independent and so is the matrix to be inverted.
-It is computed once and for all and applies to all ocean time steps.
-
%% =================================================================================================
\section[Lateral diffusion term and operators (\textit{dynldf.F90})]{Lateral diffusion term and operators (\protect\mdl{dynldf})}
\label{sec:DYN_ldf}
diff --git a/doc/latex/NEMO/subfiles/chap_SBC.tex b/doc/latex/NEMO/subfiles/chap_SBC.tex
index 7552a418..d48e5e25 100644
--- a/doc/latex/NEMO/subfiles/chap_SBC.tex
+++ b/doc/latex/NEMO/subfiles/chap_SBC.tex
@@ -1004,7 +1004,7 @@ When an external wave model (see \autoref{sec:SBC_wave}) is used in the coupled
The namelist above allows control of various aspects of the coupling fields (particularly for vectors) and
-now allows for any coupling fields to have multiple sea ice categories (as required by LIM3 and CICE).
+now allows for any coupling fields to have multiple sea ice categories (as required by SI3).
When indicating a multi-category coupling field in \nam{sbc_cpl}{sbc\_cpl}, the number of categories will be determined by
the number used in the sea ice model.
In some limited cases, it may be possible to specify single category coupling fields even when
@@ -2034,45 +2034,11 @@ the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc}{sbc}
This model computes the ice-ocean fluxes,
that are combined with the air-sea fluxes using the ice fraction of each model cell to
provide the surface averaged ocean fluxes.
- Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3} or \key{cice}).
+ Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3}).
The activation automatically overwrites the read value of nn\_ice to its appropriate value
- (\ie\ $2$ for SI3 or $3$ for CICE).
+ (\ie\ $2$ for SI3).
\end{description}
-% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
-%GS: ocean-ice (SI3) interface is not located in SBC directory anymore, so it should be included in SI3 doc
-
-%% =================================================================================================
-\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]{Interface to CICE (\protect\mdl{sbcice\_cice})}
-\label{subsec:SBC_cice}
-
-It is possible to couple a regional or global \NEMO\ configuration (without AGRIF)
-to the CICE sea-ice model by using \key{cice}.
-The CICE code can be obtained from \href{http://oceans11.lanl.gov/trac/CICE/}{LANL} and
-the additional 'hadgem3' drivers will be required, even with the latest code release.
-Input grid files consistent with those used in \NEMO\ will also be needed,
-and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used
-(seek advice from UKMO if necessary).
-Currently, the code is only designed to work when using the NCAR forcing option for \NEMO\ %GS: still true ?
-(with \textit{calc\_strair}\forcode{=.true.} and \textit{calc\_Tsfc}\forcode{=.true.} in the CICE name-list),
-or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model
-(with \textit{calc\_strair}\forcode{=.false.} and \textit{calc\_Tsfc}\forcode{=false}).
-The code is intended to be used with \np{nn_fsbc}{nn\_fsbc} set to 1
-(although coupling ocean and ice less frequently should work,
-it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly -
-the user should check that results are not significantly different to the standard case).
-
-There are two options for the technical coupling between \NEMO\ and CICE.
-The standard version allows complete flexibility for the domain decompositions in the individual models,
-but this is at the expense of global gather and scatter operations in the coupling which
-become very expensive on larger numbers of processors.
-The alternative option (using \key{nemocice\_decomp} for both \NEMO\ and CICE) ensures that
-the domain decomposition is identical in both models (provided domain parameters are set appropriately,
-and \textit{processor\_shape~=~square-ice} and \textit{distribution\_wght~=~block} in the CICE name-list) and
-allows much more efficient direct coupling on individual processors.
-This solution scales much better although it is at the expense of having more idle CICE processors in areas where
-there is no sea ice.
-
%% =================================================================================================
\subsection[Freshwater budget control (\textit{sbcfwb.F90})]{Freshwater budget control (\protect\mdl{sbcfwb})}
\label{subsec:SBC_fwb}
diff --git a/doc/latex/NEMO/subfiles/chap_cfgs.tex b/doc/latex/NEMO/subfiles/chap_cfgs.tex
index 231f4680..ca72b49c 100644
--- a/doc/latex/NEMO/subfiles/chap_cfgs.tex
+++ b/doc/latex/NEMO/subfiles/chap_cfgs.tex
@@ -289,7 +289,7 @@ namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
a regular lat-lon grid at approximately 12km horizontal resolution.
-The appropriate \textit{\&namcfg} namelist is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}.
+The appropriate \textit{\&namcfg} namelist is available in \path{./cfgs/AMM12/EXPREF/namelist_cfg}.
It is used to build the correct dimensions of the AMM domain.
This configuration tests several features of \NEMO\ functionality specific to the shelf seas.
diff --git a/doc/latex/NEMO/subfiles/chap_misc.tex b/doc/latex/NEMO/subfiles/chap_misc.tex
index a5600507..ab279184 100644
--- a/doc/latex/NEMO/subfiles/chap_misc.tex
+++ b/doc/latex/NEMO/subfiles/chap_misc.tex
@@ -198,8 +198,8 @@ open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran
then the formally correct setting for \np{open_ocean_jstart}{open\_ocean\_jstart} is 41. Using this value as
the first row to be read will result in a 362x292 domain which is the same size as the
original ORCA1 domain. Thus the extended domain configuration file can be used with all
-the original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav =
-.false.}). Full instructions for achieving this are:
+the original input files for ORCA1 if the ice cavities are not active (\np{ln_isfcav =
+.false.}). Full instructions for achieving this are:
\begin{itemize}
\item Add the new attribute to any input files requiring a j-row offset, i.e:
--
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